Related papers: Principles for optimal cooperativity in allosteric…
Lattice structures have been widely used in various applications of additive manufacturing due to its superior physical properties. If modeled by triangular meshes, a lattice structure with huge number of struts would consume massive…
Chains of resonators in the form of spring-mass systems have long been known to exhibiting interesting properties such as band gaps. Such features can be leveraged to manipulate the propagation of waves such as the filtering of specific…
Fundamental questions about the role of the quaternary structures are addressed using a statistical mechanics off-lattice model of a dimer protein. The model, in spite of its simplicity, captures key features of the monomer-monomer…
A protein model with the pairwise interaction energies varying as local environment changes, i.e., including some kinds of collective effect between the contacts, is proposed. Lattice Monte Carlo simulations on the thermodynamical…
n source and destination pairs randomly located in an area want to communicate with each other. Signals transmitted from one user to another at distance r apart are subject to a power loss of r^{-alpha}, as well as a random phase. We…
The dynamics of a folded protein is studied in water and glycerol at a series of temperatures below and above their respective dynamical transition. The system is modeled in two distinct states whereby the protein is decoupled from the bulk…
We apply a new approach to the reverse protein folding problem. Our method uses a minimization function in the design process which is different from the energy function used for folding. For a lattice model, we show that this new approach…
Cells use temporal dynamical patterns to transmit information via signaling pathways. As optimality with respect to the environment plays a fundamental role in biological systems, organisms have evolved optimal ways to transmit information.…
We analyze the performance of an interference-limited, decode-and-forward, cooperative relaying system that comprises a source, a destination, and $N$ relays, placed arbitrarily on the plane and suffering from interference by a set of…
Protein structures in nature often exhibit a high degree of regularity (secondary structures, tertiary symmetries, etc.) absent in random compact conformations. We demonstrate in a simple lattice model of protein folding that structural…
Stochastic processes offer a flexible mathematical formalism to model and reason about systems. Most analysis tools, however, start from the premises that models are fully specified, so that any parameters controlling the system's dynamics…
Faced with complex and unstructured construction environments, wheeled and tracked robots exhibit significant limitations in terrain adaptability and flexibility, making it difficult to meet the requirements of autonomous operation.…
We present the first distributed optimization algorithm with lazy communication for collaborative geometric estimation, the backbone of modern collaborative simultaneous localization and mapping (SLAM) and structure-from-motion (SfM)…
Eukaryotic cells generally sense chemical gradients using the binding of chemical ligands to membrane receptors. In order to perform chemotaxis effectively in different environments, cells need to adapt to different concentrations. We…
Materials in which electrons occupy interstitial sites as anions are called electrides and exhibit unusual dimensionality-dependent electronic behavior. These properties make electrides attractive for catalysis, transparent conductors, and…
Within periodic materials and structures, wave scattering and dispersion occur across constituent material interfaces leading to a banded frequency response. In an earlier paper, the elastodynamics of one-dimensional periodic materials and…
In this paper we theoretically investigate underlying assumptions that have been used for designing adaptive particle swarm optimization algorithms in the past years. We relate these assumptions to the movement patterns of particles…
Proteins are central to biological systems, participating as building blocks across all forms of life. Despite advancements in understanding protein functions through protein sequence analysis, there remains potential for further…
While allostery is of paramount importance for protein signaling and regulation, the underlying dynamical process of allosteric communication is not well understood. PDZ3 domain represents a prime example of an allosteric single-domain…
We carry out a theoretical study of the vibrational and relaxation properties of naturally-occurring proteins with the purpose of characterizing both the folding and equilibrium thermodynamics. By means of a suitable model we provide a full…